Thats what Im thinking.
The good news is that you had a backup of the files. Something we often neglect. Since you havent been able to reproduce the problem it must have been a combination of circumstances. We can only hope it dosent happen again.
JD, that sounds right to me. I dont use the 48 hour option and temp files are deleted regardless of creation/modified/last accessed dates. I think the guide needs to be updated to reflect this.